本文整理汇总了Python中simtk.openmm.CustomGBForce类的典型用法代码示例。如果您正苦于以下问题：Python CustomGBForce类的具体用法？Python CustomGBForce怎么用？Python CustomGBForce使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了CustomGBForce类的13个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: __init__
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
CustomGBForce.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("alpha")
self.addPerParticleParameter("beta")
self.addPerParticleParameter("gamma")
self.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
self.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))
self.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"radius1=or1+offset; radius2=or2+offset;"
"neckScale=0.826836; neckCut=0.68; offset=0.0195141", CustomGBForce.ParticlePairNoExclusions)
self.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
_createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)示例2: GBSAOBC2Force
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom示例3: setParticleParameters
def setParticleParameters(self, idx, params):
params = copy.deepcopy(params)
params[self.RADIUS_ARG_POSITION] = strip_unit(params[self.RADIUS_ARG_POSITION], u.nanometer) - self.OFFSET
params[self.SCREEN_POSITION] *= params[self.RADIUS_ARG_POSITION]
CustomGBForce.addParticle(self, params)
return params示例4: GBSAGBn2Force
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
custom.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
custom.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"radius1=or1+offset; radius2=or2+offset;"
"neckScale=0.826836; neckCut=0.68; offset=0.0195141", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)
return custom示例5: GBSAOBC1Force
def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*excl*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"excl=step(abs(q1)-0.00000001)*step(abs(q2)-0.00000001);" # exclude pair where one atom is not charged
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(0.8*psi+2.909125*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff)
return custom示例6: GBSAGBnForce
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68)
custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa)
return custom示例7: GBSAGBn2Force
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.0195141)
custom.addGlobalParameter("neckScale", 0.826836)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ivdw=step(r+sr2-or1)*excl*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"excl=step(abs(q1)-0.00000001)*step(abs(q2)-0.00000001);" # exclude pair where one atom is not charged
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff)
return custom示例8: GBSAGBnForce
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
custom.addGlobalParameter("solventDielectric", solventDielectric);
custom.addGlobalParameter("soluteDielectric", soluteDielectric);
custom.addGlobalParameter("offset", 0.009)
custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
if SA=='ACE':
custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
elif SA is not None:
raise ValueError('Unknown surface area method: '+SA)
custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
return custom示例9: GBSAOBC2Force
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa)
return custom示例10: GBSAOBC2Force
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
custom.addGlobalParameter("solventDielectric", solventDielectric);
custom.addGlobalParameter("soluteDielectric", soluteDielectric);
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
if SA=='ACE':
custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
elif SA is not None:
raise ValueError('Unknown surface area method: '+SA)
custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
return custom示例11: GBSAHCTForce
def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q");
custom.addPerParticleParameter("radius");
custom.addPerParticleParameter("scale");
custom.addGlobalParameter("solventDielectric", solventDielectric);
custom.addGlobalParameter("soluteDielectric", soluteDielectric);
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-I);"
"or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff)
return custom示例12: _addParticles
def _addParticles(self):
for p in self.parameters:
radIndex = self._radiusToIndex[p[self.RADIUS_ARG_POSITION]]
CustomGBForce.addParticle(self, p + [radIndex])示例13: __init__
def __init__(self):
CustomGBForce.__init__(self)
self.parameters = []